Intersect is Operational
by Selonianth
Summary: Takes place Season 2 episode 1. What might've happened had the intersect not gone boom. Two Endings. Character Death


Disclaimer: Don't own Chuck.

Summary: Takes place Season 2 episode 1. What might've happened had the intersect not gone boom. Two Endings.

* * *

Chuck knew the General and Agent Graham were lying when they told him he could have a regular life once the new Intersect was up. He'd already been told that it was impossible to ever get the old one out of his head and by that logic he knew he would always be in danger of being captured and tortured for information or simply forced to aid some terrorist group somewhere.

He'd acted all relieved that it would finally be over but he wasn't entirely sure it would be, not while he was alive.

A knock at the door drew his attention as he tried to think about how he would try to protect himself and he walked to answer it, knowing it would probably be Sarah with the news that he was free. The chance to finally get a real shot at her was the one good thought that was running through his head, even if it would mean being on the run for the rest of his life.

He opened the door to the smiling face of the beautiful woman he'd fallen for in such a short time, "Hey Sarah, what's the news?"

"The Intersect is up, you're free," Sarah smiled, her smile freezing when they both heard the distinctive sound of a hammer being pulled back on a gun.

Hearing the hammer Chuck was, somewhat relieved. "That you Casey?" He called out, getting only a grunt in reply.

"So, Beckman and Graham sent you to end the danger of me running around huh. I suppose it's better than running for the rest of my life, we all know there's no way of just removing the intersect images from my brain. I will be in danger for the rest of my life of being captured and used against the people I care about, in danger of being tortured, and definitely in danger of being killed if my usefulness reached an end," Chuck spoke, shaking his head.

Sarah looked into his eyes and her hand inched toward her pistol. She wasn't about to-

"It's ok Sarah. I do have one thing to ask first though Casey."

Casey, having barely managed to get the courage to sneak into Chuck's apartment in the first place, was beginning to tremble. He understood how important it was that there not be a walking, talking, intersect running around. It was dangerous both for the intersect and the country, but Chuck was... well, Casey wouldn't call him a friend but he was a comrade. The man had been a whiny civilian when they'd first met and though he still loved to throw the rulebook out the window he was becoming a truly great person to work with. He could certainly let Chuck have one last request, it was the least he could do. "Go ahead."

"I'm sure you guys hooked up our tv in here to the network right? Could you call the good General for me? My last request kinda needs her help."

Sarah wordlessly walked over and engaged the communications section of the room unable to look at Chuck. The screen changed to show General Diane Beckman with a raised eyebrow, "Yes?"

* * *

Ending One Starts.

"General, I know you sent Casey to kill me, eliminating the danger I pose willingly or not to national security. I'm not going to run for it, I wouldn't get away anyway, I do have one thing to ask though, and as far as I can see it's the least you can do."

The general's face softened temporarily before she nodded, "Go ahead Mr Bartowski, I will do what I can. You've served this country well and you're correct, you deserve at least this much."

"I want my family taken care of, financially and security-wise. That's all I ask," the human intersect said, refusing to look anywhere but the General's face.

The general took a moment, "Agreed."

Sarah stepped into the frame, "General, I'd like to volunteer as the protection for his family. I would have an iron-clad cover and I feel I could do no less."

The general eyed the CIA agent and an eyebrow was raised. She looked up and Graham stepped into frame on the other side of the call. "Permission granted, your mission until further notice is the protection of Mr Bartowski's family."

The call ended and Chuck finally turned to look at Sarah, "I love you. You know that don't you."

"I love you too, really," Sarah replied kissing him once more before she backed up with a sad smile on her face.

Chuck turned again to face Casey, "It's ok Casey. Really, it is. Some things have to be done."

Casey nodded and steeled himself before his finger pulled the trigger.

* * *

The funeral was small but well done, most of Chuck's co-workers from the Buy More were present, even Jeff looked remarkably cleaned up for the occasion. Only one was missing, John Casey. The other workers passed it off as not having known Chuck for very long, Sarah knew better. The NSA agent had left town immediately after shooting Chuck to take the time to get over shooting the man. He'd never lost a wink of sleep over shooting traitors and enemies of the state, but killing Chuck had done a number on the angry NSA spy.

Sarah was standing with the family, she'd attempted to stand apart but Elle had dragged her over and forced her to stand with them. She was family, the grieving sister had said, her brother loved her and she had already started counting the blond as her future sister-in-law.

Sarah was also the only one who knew that the funeral, paid for by a life insurance plan that said it was taken out the year previous, was really being paid for by the government, and the lottery ticket they'd found in Chuck's room was planted giving the family five thousand dollars a month for the next sixty years.

She would follow Chuck's last wish and protect his family, she may not have been able to tell him till right before he died that she loved him, but she would damn well follow his final wish.

* * *

Ending Two Starts.

"General, I-" Chuck started, stopping when he felt Casey's hand on his shoulder.

"General, I cannot in good conscience follow my current orders. I won't kill Chuck Bartowski, and I won't let you send anyone else to do it either."

"What do you propose we do Major Casey?"

"Continue as normal. Just because the new Intersect is up doesn't mean that it catches everything, or that there aren't things that only a mobile Intersect could do. I know the situations the Intersect normally comes in handy. I also know that roughly half of our missions have been the kind of task it does not shine at. My suggestion, General, is that we put Chuck through crash course training and we continue as a full time team."

The general changed her gaze from Casey to Chuck and then to Sarah. "Agent Walker, do you agree with this course of action?"

Sarah took a moment to think, a glance at Chuck made her decision for her. "Yes ma'am, I do. Chuck's methods may be unorthodox but we have not failed yet because of him."

"Very well. You have your orders. Carry them out."


End file.
